There are various medical and cosmetic procedures that may be performed now using various degrees of automation, in some instances using hand-held automated tools, in other instances utilizing automated systems that may include robotic arms, for example. No matter what the level of automation, it is important that the user ensures that the cannula or needles are maintained at the required level of cleanliness, so that they do not contribute to infections or other such contamination issues of the patient or associated equipment. One such medical procedure is hair transplantation. Hair transplantation is a highly repetitive, time consuming and tedious procedure that can last many hours (e.g. whole day), and therefore the development of an image-guided robotic system for follicular unit extraction and implantation has been proposed, for example, in the commonly-assigned U.S. Patent Publication No. 2007/0106306 to Bodduluri et al. The Bodduluri et al. '306 publication discloses a robotic system for harvesting and/or implanting FUs having a robotic arm and a tool (e.g. harvesting cannula or punch) operatively attached to the robotic arm. A robotic arm is positioned relative to a patient, so that a targeted body surface (in this instance, the donor area on the back of a patient's scalp) is within reach of a harvesting or implanting tool. The robotic system may include one or more cameras, and a processor receives and processes the images acquired thereby. A controller operatively associated with the processor precisely maneuvers the robotic arm to position the tool at desired locations and in desired orientations, for example, relative to follicular units targeted for harvesting from the scalp or at the desired implantation locations and orientations.